Some of the greatest breakthroughs in biomedical research may be attributed to the development of the numerous high throughput technologies for the quantitative measurements of biomolecules. Many of these technologies are made possible by microfabrication techniques commonly used in the semiconductor industry. For example, DNA and protein arrays fabricated by robotic printing and photolithographic methods have enabled extremely large-scale surveys of biomolecules (see, Fodor, S. P. A.; Read, J. L.; Pirrung, M. C.; Stryer, L.; Lu, A. T.; Solas, D. Science 1991, 251, 767-773; Schena, M.; Shalon, D.; Davis, R. W.; Brown, P. O. Science 1995, 270, 467-470; Lockhart, D. J.; Dong, H.; Byrne, M. C.; Follettie, M. T.; Gallo, M. V.; Chee, M. S.; Mittmann, M.; Wang, C.; Kobayashi, M.; Horton, H., et al. Nat. Biotechnol. 1996, 14, 1675-1680; Zhu, H.; Bilgin, M.; Bangham, R.; Hall, D.; Casamayor, A.; Bertone, P.; Lan, N.; Jansen, R.; Bidlingmaier, S.; Houfek, T., et al. Science 2001, 293, 2101-2105). The emerging “next generation” genome sequencing technologies, many of which utilize massive parallelization and miniaturization to achieve unprecedented multiplexing, throughput and cost reductions, promise to revolutionize biomedical research and enable personalized healthcare (see, Emrich, C. A.; Tian, H.; Medintz, I. L.; Mathies, R. A. Anal. Chem. 2002, 74, 5076-5083; Margulies, M.; Egholm, M.; Altman, W. E.; Attiya, S.; Bader, J. S.; Bemben, L. A.; Berka, J.; Braverman, M. S.; Chen, Y. J.; Chen, Z., et al. Nature 2005, 437, 376-380; Shendure, J.; Porreca, G. J.; Reppas, N. B.; Lin, X.; McCutcheon, J. P.; Rosenbaum, A. M.; Wang, M. D.; Zhang, K.; Mitra, R. D.; Church, G. M. Science 2005, 309, 1728-1732; Bentley, D. R. Curr. Opin. Genet. Dev. 2006, 16, 545-552; Church, G. M. Sci. Am. 2006, 294, 46-54; Johnson, D. S.; Mortazavi, A.; Myers, R. M.; Wold, B. Science 2007, 316, 1497-1502). Some of these technology platforms utilize randomly distributed DNA-conjugated microbeads or clones on a glass slide within a reaction chamber. The random arrangements of the beads or clones however, result in low throughput and imaging efficiency, complicated image processing and high reagent costs.
One approach to dramatically improve these devices involves the use of microfabricated arrays to eliminate overlap and to minimize the area between the beads or clones. Such arrays may be generated by depositing samples onto glass slides using robotic contact printing, micro-contact printing or dip pen lithography (see, Schena, M.; Shalon, D.; Davis, R. W.; Brown, P. O. Science 1995, 270, 467-470; Thibault, C.; Berm, V. L.; Casimirius, S.; Trévisiol, E.; Francois, J.; Vieu, C. J. Nanobiotech. 2005, 3, 1-12; Pla-Roca, M.; Fernandez, J. G.; Mills, C. A.; Martinez, E.; Samitier, J. Langmuir 2007, 23, 8614-8618; Tan, H.; Huang, S.; Yang, K. L. Langmuir 2007, 23, 8607-8613; Nam, J.-M.; Han, S. W.; Lee, K.-B.; Liu, X.; Rathner, M. A.; Mirkin, C. A. Angew). These arrays may also be generated by assembling beads onto microfabricated arrays of wells on glass or silicon substrates, or in etched wells on the face of a fiber-optic bundle (see, Xia, Y.; Yin, Y.; Lu, Y.; McLellan, J. Adv. Funct. Mater. 2003, 13, 907-918; Michel, R.; Reviakine, I.; Sutherland, D.; Fokas, C.; Csucs, G.; Danuser, G.; Spencer, N. D.; Textor, M. Langmuir 2002, 18, 8580-8586; Cui, Y.; Bjork, M. T.; Liddle, J. A.; Sonnichsen, C.; Boussert, B.; Alivisatos, A. P. Nano Lett. 2004, 4, 1093-1098; Steemers, F. J.; Gunderson, K. L. Biotechnol. J. 2007, 2, 41-49; Michael, K. L.; Taylor, L. C.; Schultz, S. L.; Walt, D. R. Anal. Chem. 1998, 70, 1242-1248; Ferguson, J. A.; Steemers, F. J.; Walt, D. R. Anal. Chem. 2000, 72, 5618-5624) Since bead assembly may not occur in an efficient and reliable manner if the process depends solely upon gravitational forces and Brownian motion, this process is typically achieved via solvent evaporation or de-wetting (see, Cui, Y.; Bjork, M. T.; Liddle, J. A.; Sonnichsen, C.; Boussert, B.; Alivisatos, A. P. Nano Lett. 2004, 4, 1093-1098; Steemers, F. J.; Gunderson, K. L. Biotechnol. J. 2007, 2, 41-49; Michael, K. L.; Taylor, L. C.; Schultz, S. L.; Walt, D. R. Anal. Chem. 1998, 70, 1242-1248; Ferguson, J. A.; Steemers, F. J.; Walt, D. R. Anal. Chem. 2000, 72, 5618-5624; Yin, Y.; Lu, Y.; Gates, B.; Xia, Y. J. Am. Chem. Soc. 2001, 123, 8718-8729). These approaches however, are not suitable when rapid assembly is required or sample drying is undesirable.
Other groups have employed electric and magnetic assembly methods to overcome these issues, but these active approaches require multi-step fabrication processes and complex field generation schemes (see, Li, A. X.; Seul, M.; Cicciarelli, J.; Yang, J. C.; Iwaki, Y. Tissue Antigens 2004, 63, 518-528; Wen, W.; Wang, N.; Zheng, D. W.; Chen, C.; Tu, K. N. J. Mater. Res. 1999, 14; Roberts, L. A.; Crawford, A. M.; Zappe, S.; Jain, M.; White, R. L. IEEE Trans. Magnet. 2004, 40, 3006-3008; Yellen, B. B.; Friedman, G. Langmuir 2004, 20, 2553-2559).
For many genomic and proteomic applications however, the array fabrication and assembly processes also need to be scalable and inexpensive, and the format of the arrays must also be compatible with high-throughput imaging and micro-fluidic devices. Thus, there remains a need in the art for improved high throughput technologies for biomolecules.